Comments:

Wizard 1 Ninja 3? WHY????? Ninja 1 Wizard 3 is MUCH stronger, more flexable, and still actually has a chance to be useful later levels unlike Ninja (note this does not apply to ninjas who multiclass drunken master monk for unlimited KI)

Ninja 3 gives a ninja trick and 2d6 sneak attack.
Wizard 3 certainly allows casting of useful 2nd level spells... like invisibility, but that could also be a ninja trick.
Plus, Wizards don't get many skill points, even with their high intelligence they will get the same as a normal intelligence ninja

the only skills a wizard/ninja need are disable device stealth and perception. well within the skillpoints they're getting, no ninja trick is worth a 2nd lv spell slot a second sneak attack die means almost nothing when you're already down so much bab that your attacks wont hit anyway.